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The opening of a massive sewage holding tank under South Boston today will complete a transformation of Boston Harbor that was almost unimaginable three decades ago: The city’s once-fouled beaches are now so clean that swimmers can dive in virtually every summer day.

The 2.1-mile-long tank under Day Boulevard will temporarily store up to 19 million gallons of waste water that would otherwise overwhelm the sewer system when it rains, sending untreated sewage into the harbor off South Boston and Dorchester. The dirty water collected in the holding tunnel will be pumped to the Deer Island Sewage Treatment Plant once storms pass.

The result, according to government officials? Instead of an average of eight beach closures each summer, there will be, at most, an average of one in five years.

“Now, parents can let their kids swim even after a rainstorm without the fear of getting diseases,’’ said Peter Shelley, senior counsel of the Conservation Law Foundation, a Boston-based environmental group that 28 years ago filed one of the main lawsuits demanding that the harbor be cleaned. “We did this so people can use the harbor.’’

Said Massachusetts Water Resources Authority executive director Fred Laskey: “It really will be among the cleanest urban beaches in America.’’

The $225 million tunnel is one of the last major pieces of the nearly $5 billion harbor recovery — and one of its most controversial because of its location and cost. Advocates have long celebrated the harbor’s renaissance, evident in the return of clammers who dig in urban sands, the disappearance of tumors on fish, and a building boom on its shores. But the water still wasn’t always safe at the city’s most popular beaches.

The problem was twofold. During particularly heavy storms, raw human sewage and storm water mixed in the labyrinth of pipes under Boston. When the sewer system became overwhelmed — about 20 times a year — the bacteria-filled soup poured into the harbor.

During more moderate rains, storm water runoff, carrying animal waste, sewage from illegal hookups, debris, and lawn fertilizer, also flowed into the harbor 105 times a year, on average.

If bacteria counts were high enough during the summer, beaches also closed. During the winter, the releases were believed harmful to marine life.

Now, MWRA officials say, the combination of sewage and storm water will flow into the harbor on average once every 25 years. Storm water alone will enter the South Boston area on average only once every five years, they predict.

The harbor cleanup is still not done; intensive work continues to clean the Charles, Mystic, and other rivers that flow into the harbor. But those projects will have a negligible effect on swimming quality in South Boston and Dorchester.

The turnaround is stunning for beaches once so littered with condoms that flowed out of sewage pipes that they earned the nickname “Charles River whitefish.’’ Visitors would complain their feet smelled after wading in the harbor.

A Quincy attorney fed up with jogging through sewage grease on Quincy’s Wollaston Beach helped file the first suit to clean the harbor in 1982. The Conservation Law Foundation soon filed a federal suit and in 1985, a federal judge ordered a full cleanup.

The cost forced double-digit rate hikes for MWRA customers, and protests abounded. Today, Joseph Favaloro of the MWRA advisory board, the fiscal watchdog of the agency, says it is hard to tease out exactly how much the average ratepayer has paid for the cleanup because costs have been spread over 30 years and so many other improvements in the system have been made. The federal government also contributed more than $800 million.

As advocates began pushing for South Boston and Dorchester beaches to be made usable, it became clear storm water had to be treated in addition to sewage.

As part of the court case, the MWRA agreed to build a treatment facility in South Boston that would include storm water. But it was a sore point with agency officials, who argued that they were in the sewage — not storm water — business and that all the work would not prevent beaches from being closed because of illegal sewage pipes or animal waste that could still flow into the harbor.

In 2000, South Boston residents balked at the proposed site for the treatment facility, while some harbor advocates began debating whether the water was clean enough and whether it would be too expensive to make it cleaner.

But in 2005, US District Judge Richard G. Stearns ordered the tunnel to be built, with a smaller pumping station, by mid-2011.

Now, when heavy rains approach, gates will direct storm water and any combined sewage and storm water into the tunnel to wait out the storm.

For beachgoers this week along Carson Beach, the idea of a summer with no worries about water quality — and the flags that warn when swimming is unsafe — was a welcome relief.

“I’ve been coming here since I was little, and the beach has changed so much’’ for the better, said Linda Doolin of Dorchester as she watched her 6-year-old niece splash in the water Tuesday. “It should be as clean as it can get. So many people come here.’’

Environmental Protection Agency regional administrator Curt Spalding, whose agency was a major plaintiff in the case, called today’s milestone “one of the most important the EPA has accomplished anywhere in the country.’’

State Energy and Environmental Affairs Secretary Richard K. Sullivan Jr., whose departments have worked to improve urban beach facilities and access, said “this is a great example of what good things can be done when citizens get involved and government makes strategic and important investments.’’

With rain in the forecast today, Bruce Berman of Save the Harbor/Save the Bay, an advocacy group that pushed for the cleanup, said that for the first time in decades, people will be able to swim in the rain and know the water is safe.

“Stories about infrastructure are often the least sexy stories,’’ he said, “but at the end of the day, this project has a very real, positive, and dramatic effect on quality of life in Boston.’’